Mailman 3 November 2008 - SciPy-User

F2PY: Problems after upgrading to Python2.6
by Benjamin Kern 19 Nov '08

19 Nov '08

Hello, i'm experiencing strange problems after upgrading to python2.6. I'm also using numpy-svn and scipy-svn. So here is the problem. When i try to wrap the following simple fortran code, C File hello.f subroutine foo (a) integer a print*, "Hello from Fortran!" print*, "a=",a end I have problems executing this from python, i.e. >>> import hello >>> print hello.__doc__ This module 'hello' is auto-generated with f2py (version:2_5968). Functions: foo(a) . >>> print hello.foo.__doc__ foo - Function signature: foo(a) Required arguments: a : input int >>> hello.foo(4) Traceback (most recent call last): File "<stdin>", line 1, in <module> RuntimeError: more argument specifiers than keyword list entries (remaining format:'|:hello.foo') Thanks for the help in advance

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array manipulation
by Nils Wagner 19 Nov '08

19 Nov '08

Hi all, How can I insert a row/column in an existing array ? Nils

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how to get only complete years from series?
by Timmie 18 Nov '08

18 Nov '08

Hello, I am unsing the scikit.timeseries to evaluate a long-term measurement data set. How can I extract those years, which have complete measurements? In the below, years 2004 & 2008 are not complete. Is there a generic possibility that all incomplete years get masked? Thanks & regards, Timmie ###code import numpy as np import numpy.ma as ma import scikits.timeseries as ts data = np.arange(0, 40800) start_dt = ts.Date(freq='H', year=2004, month=3, day=1, hour=0) s_all = ts.time_series(data, freq='H', start_date=start_dt)

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a sequence of formats in savetxt
by Nils Wagner 18 Nov '08

18 Nov '08

Hi all, How do I specify a sequence of formats in savetxt ? savetxt('f06.dat',F,fmt='%10.5f %i4 4%10.5f') doesn't work F is an (m,5) array. The entries of the second column should be stored as integers. Nils

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why signature of func in odeint != ode ?
by Emanuele Olivetti 18 Nov '08

18 Nov '08

Why signature of func in odeint is swapped (y,t0 -> t0,y) with respect to func in ode ? It would be nice to have same signature in order to be able to play with both of them more transparently. Details from docstrings: scipy.integrate.odeint: ---- Inputs: func -- func(y,t0,...) computes the derivative of y at t0. ---- scipy.integrate.ode: ---- where f and jac have the following signatures: def f(t,y[,arg1,..]): return <f(t,y)> ---- Is there a reason for this or is it just a little defect? Regards, Emanuele

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Re: [SciPy-user] weave problem on ubuntu 8.10
by Kristian Hans Sandberg 17 Nov '08

17 Nov '08

That's exactly the problem I wrote about a couple of days ago (with topic "weave/blitz problem"). It's listed as Ticket # 739 in the scipy trac system: http://www.scipy.org/scipy/scipy/ticket/739 This seems to happen with g++ version 4.3. As a temporary fix, I installed g++ version 4.2, and then it worked. I believe this problem will be more common as more people update to newer compilers. Kristian Kristian Sandberg, Ph.D. Dept. of Applied Mathematics and The Boulder Laboratory for 3-D Electron Microscopy of Cells University of Colorado at Boulder Campus Box 526 Boulder, CO 80309-0526, USA Phone: (303) 492 0593 (work) (303) 499 4404 (home) (303) 547 6290 (cell) Home page: http://amath.colorado.edu/faculty/sandberg ---- Original message ---- >Date: Mon, 17 Nov 2008 11:18:30 -0500 >From: "Bobby H. Braswell" <rob.braswell(a)unh.edu> >Subject: Re: [SciPy-user] weave problem on ubuntu 8.10 >To: SciPy Users List <scipy-user(a)scipy.org> > > Hi, thanks for the reply. Here are the first lines: > > <weave: compiling> > In file included from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/applics.h:400, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vecexpr.h:32, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vecpick.cc:16, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vecpick.h:293, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/vector.h:449, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/tinyvec.h:430, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array-impl.h:44, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array.h:32, > from > /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:11: > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/mathfunc.h: > In static member function `static long int > blitz::_bz_abs<long int>::apply(long int)': > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/mathfunc.h:45: > error: `labs' is not a member of `std' > In file included from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array/funcs.h:29, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array/newet.h:29, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array/et.h:27, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array-impl.h:2515, > from > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/array.h:32, > from > /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:11: > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h: > In static member function `static int > blitz::Fn_abs<int>::apply(int)': > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:509: > error: call of overloaded `abs(int&)' is ambiguous > /usr/include/c++/4.3/cmath:99: note: candidates are: > double std::abs(double) > /usr/include/c++/4.3/cmath:103: > note: float std::abs(float) > /usr/include/c++/4.3/cmath:107: > note: long double std::abs(long > double) > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h: > In static member function `static long int > blitz::Fn_abs<long int>::apply(long int)': > /usr/lib/python2.5/site-packages/scipy/weave/blitz/blitz/funcs.h:530: > error: `labs' is not a member of `std' > /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp: > In function `char* find_type(PyObject*)': > /home/braswell/.python25_compiled/sc_f935818f52299953943b3b48fe3685483.cpp:35: > warning: deprecated conversion from string constant > to `char*' > ... > > On Mon, 2008-11-17 at 17:08 +0100, So/ren Nielsen > wrote: > > Hi Rob, > > What are the first lines of your error message? > > I found the answer to my own question... I just > had to add type_converters = converters.blitz > under the ext_function. > > On Mon, Nov 17, 2008 at 4:18 PM, Bobby H. Braswell > <rob.braswell(a)unh.edu> wrote: > > Hi- > > By coincidence I am trying to get weave working > on a new system, I had previously been using it > successfully under OS X with the Fink version of > SciPy. I don't want to distract from Soren's > question but when I try his simple example (or > any of my own) using converters.blitz, I get a > very long error message, actually mostly > warnings, but it ends like this: > > >>> ravg = weave.inline(code, ['xlen', 'ylen', > 'test'], type_converters=converters.blitz, > compiler = 'gcc') > ...hundreds of lines... > Traceback (most recent call last): > File "<stdin>", line 2, in <module> > File > "/usr/lib/python2.5/site-packages/scipy/weave/inline_tools.py", > line 339, in inline > **kw) > File > "/usr/lib/python2.5/site-packages/scipy/weave/inline_tools.py", > line 447, in compile_function > verbose=verbose, **kw) > File > "/usr/lib/python2.5/site-packages/scipy/weave/ext_tools.py", > line 365, in compile > verbose = verbose, **kw) > File > "/usr/lib/python2.5/site-packages/scipy/weave/build_tools.py", > line 269, in build_extension > setup(name = module_name, ext_modules = > [ext],verbose=verb) > File > "/usr/lib/python2.5/site-packages/numpy/distutils/core.py", > line 184, in setup > return old_setup(**new_attr) > File "/usr/lib/python2.5/distutils/core.py", > line 168, in setup > raise SystemExit, "error: " + str(msg) > scipy.weave.build_tools.CompileError: error: > Command "g++ -pthread -fno-strict-aliasing > -DNDEBUG -g -fwrapv -O2 -fPIC > -I/usr/lib/python2.5/site-packages/scipy/weave > -I/usr/lib/python2.5/site-packages/scipy/weave/scxx > -I/usr/lib/python2.5/site-packages/scipy/weave/blitz > -I/usr/lib/python2.5/site-packages/numpy/core/include > -I/usr/include/python2.5 -c > /home/braswell/.python25_compiled/sc_f8b4f30889557b51310ac43eda9472b30.cpp > -o > /tmp/braswell/python25_intermediate/compiler_a9bbef2f14d61f7aa8f0ba6e068e18c2/home/braswell/.python25_compiled/sc_f8b4f30889557b51310ac43eda9472b30.o" > failed with exit status 1 > > Sorry if this is more of a compiler/Ubuntu > problem, I'm not sure about that. I'd be > grateful to hear from someone who has had or not > had problems with Weave on Ubuntu 8.10. > > Thanks very much, > Rob > > On Mon, 2008-11-17 at 15:40 +0100, So/ren > Nielsen wrote: > > Can anyone explain why this fails? This piece > of code runs perfectly using weave.inline and > type_converters = blitz.. > > Obviously it can't handle 2D arrays anymore. > It's just a stupid example to illustrate that. > > Thanks, > Soren > > CODE : > ------------------------------------------------------------------------------------------------ > mod = ext_tools.ext_module('ravg_ext') > > test = zeros((5,5)) > xlen = 5 > ylen = 5 > > code = """ > int x, y; > > for( x = 0; x < xlen; x++) > { > for( y = 0; y < ylen; y++) > { > test(x,y) = 2; > } > } > > """ > > ravg = ext_tools.ext_function('ravg', code, > ['xlen', 'ylen', 'test']) > mod.add_function(ravg) > mod.compile(compiler = 'gcc') > > RESULT: > ------------------------------------------------------------------------------------------------ > C:\Temp\ravg_ext.cpp: In function `PyObject* > ravg(PyObject*, PyObject*, PyObject*)': > C:\Temp\ravg_ext.cpp:654: error: `test' cannot > be used as a function > C:\Temp\ravg_ext.cpp:641: warning: unused > variable 'Ntest' > C:\Temp\ravg_ext.cpp:642: warning: unused > variable 'Stest' > C:\Temp\ravg_ext.cpp:643: warning: unused > variable 'Dtest' > > Traceback (most recent call last): > File "C:\Temp\ravg_extension.py", line 132, > in ? > build_ravg_extension() > File "C:\Temp\ravg_extension.py", line 125, > in build_ravg_extension > mod.compile(compiler = 'gcc') > File > "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py", > line 365, in compile > verbose = verbose, **kw) > File > "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py", > line 269, in build_extension > setup(name = module_name, ext_modules = > [ext],verbose=verb) > File > "C:\Python24\Lib\site-packages\numpy\distutils\core.py", > line 184, in setup > return old_setup(**new_attr) > File "C:\Python24\Lib\distutils\core.py", > line 166, in setup > raise SystemExit, "error: " + str(msg) > CompileError: error: Command "g++ -mno-cygwin > -O2 -Wall > -IC:\Python24\lib\site-packages\scipy\weave > -IC:\Python24\lib\site-packages\scipy\weave\scxx > -IC:\Python24\lib\site-packages\numpy\core\include > -IC:\Python24\include -IC:\Python24\PC -c > C:\Temp\ravg_ext.cpp -o > c:\docume~1\ssn\locals~1\temp\ssn\python24_intermediate\compiler_894ad5ed761bb51736c6d2b7872dc212\Releas > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.org > http://projects.scipy.org/mailman/listinfo/scipy-user > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.org > http://projects.scipy.org/mailman/listinfo/scipy-user > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.org > http://projects.scipy.org/mailman/listinfo/scipy-user >________________ >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.org >http://projects.scipy.org/mailman/listinfo/scipy-user

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PyGSL with numpy?
by Russell E. Owen 17 Nov '08

17 Nov '08

I'm part of a project that is doing scientific computing with a mix of C++ and python (all the heavy lifting being done in C++ for speed). We need a scientific library that can be used in C++ (which puts out scipy) and preferably can also be used in python. We're considering GSL, which has a python wrapper (PyGSL), the latter of which apparently works with numpy. Has anyone tried this? How is the integration? Are there other solutions we should be considering? Regards, -- Russell

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Ext_tools converters not working??
by Søren Nielsen 17 Nov '08

17 Nov '08

Can anyone explain why this fails? This piece of code runs perfectly using weave.inline and type_converters = blitz.. Obviously it can't handle 2D arrays anymore. It's just a stupid example to illustrate that. Thanks, Soren CODE : ------------------------------------------------------------------------------------------------ mod = ext_tools.ext_module('ravg_ext') test = zeros((5,5)) xlen = 5 ylen = 5 code = """ int x, y; for( x = 0; x < xlen; x++) { for( y = 0; y < ylen; y++) { test(x,y) = 2; } } """ ravg = ext_tools.ext_function('ravg', code, ['xlen', 'ylen', 'test']) mod.add_function(ravg) mod.compile(compiler = 'gcc') RESULT: ------------------------------------------------------------------------------------------------ C:\Temp\ravg_ext.cpp: In function `PyObject* ravg(PyObject*, PyObject*, PyObject*)': C:\Temp\ravg_ext.cpp:654: error: `test' cannot be used as a function C:\Temp\ravg_ext.cpp:641: warning: unused variable 'Ntest' C:\Temp\ravg_ext.cpp:642: warning: unused variable 'Stest' C:\Temp\ravg_ext.cpp:643: warning: unused variable 'Dtest' Traceback (most recent call last): File "C:\Temp\ravg_extension.py", line 132, in ? build_ravg_extension() File "C:\Temp\ravg_extension.py", line 125, in build_ravg_extension mod.compile(compiler = 'gcc') File "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py", line 365, in compile verbose = verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py", line 269, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "C:\Python24\Lib\site-packages\numpy\distutils\core.py", line 184, in setup return old_setup(**new_attr) File "C:\Python24\Lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) CompileError: error: Command "g++ -mno-cygwin -O2 -Wall -IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include -IC:\Python24\PC -c C:\Temp\ravg_ext.cpp -o c:\docume~1\ssn\locals~1\temp\ssn\python24_intermediate\compiler_894ad5ed761bb51736c6d2b7872dc212\Releas

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f2py: Adding F_WRAPPEDFUNC to*module.c without actually wrapping a function
by Berthold "Höllmann" 17 Nov '08

17 Nov '08

I am wrapping some LAPACK routines currently not handled in scipy.linalg. some of them require workspace. In order to provide the optimal workspace i wrote some helper routines taking the FORTRAN code for calculating the optimal workspace and translating them C, e.g.:: static int dsytrf_lwork(int n, char uplo) { int one = 1; int name_len = 6; int opts_len = 1; int none = -1; int nb; (*F_WRAPPEDFUNC(ilaenv,ILAENV))(&nb, &one, "DSYTRF", &uplo, &n, &none, &none, &none, name_len, opts_len); return (n*nb); } and then in the wraper code for dsytrf:: integer intent(hide), depend(n, uplo) :: lwork = dsytrf_lwork(n, *uplo) This requires the function wrapper for the FORTRAN ilaenv function:: extern void F_WRAPPEDFUNC(ilaenv,ILAENV)(int*,int*,string,string,int*,int*,int*,int*,size_t,size_t); Now my code only works when I also wrap the ilanev function (or, I guess, any other function), otherwise the F_WRAPPEDFUNC is missing in the generated code. Is there a way to get the F_WRAPPEDFUNC macro to the wrapper code without wrapping a function? the ilanev function should not become part of the interface, nor is there any other function that should. Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: berthold.hoellmann(a)gl-group.com Internet: http://www.gl-group.com

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Shift the rows of a matrix
by Roger Herikstad 16 Nov '08

16 Nov '08

Hi list, I was curious if anyone has a good method of shifting individual rows of a matrix? My problem is that I have a matrix consisting of waveforms on the rows, and I want to shift each waveform, i.e. pad with zeros on either end, depending on where the minimum point of each waveform is located relative to a pre-determined zero point. For example, if each waveform consists for 32 data points, I would be interested in aligning each waveform so that the minimum point always happens on index 10. My current solution is to loop through each waveform and taking the dot product with a shift matrix, but I'd rather avoid the for loop if possible. If anyone has any thoughts, I'd be happy for any input. Thanks! ~ Roger

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